ARCH3D: A foundation model for global genome architecture

This repository contains the checkpoints

• pretrained.ckpt: Pre-trained ARCHED with the pre-training task head
• enhanced.ckpt: ARCH3D fine-tuned for resolution enhancement
• hyperedge.ckpt: ARCH3D with a task head for predicting hyperedges

If you use this model in your work, please cite:

Galioto, Nicholas, et al. "ARCH3D: A foundation model for global genome architecture." bioRxiv (2026): 2026-02.

@article{galioto2026arch3d,
  title={{ARCH3D}: A foundation model for global genome architecture},
  author={Galioto, Nicholas and Stansbury, Cooper and Gorodetsky, Alex Arkady and Rajapakse, Indika},
  journal={bioRxiv},
  pages={2026--02},
  year={2026},
  publisher={Cold Spring Harbor Laboratory}
}